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Add ruff pre-commit and account for it
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‎.github/workflows/cd.yml‎

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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: docs/build
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‎.github/workflows/ci.yml‎

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run: |
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python -c "import pytest; print('pytest', pytest.__version__)"
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python -c "import pydocstyle; print('pydocstyle', pydocstyle.__version__)"
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- name: Run tests
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run: python -m pytest --pydocstyle
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- name: Run linting tests
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run: |
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black --check .

‎.github/workflows/deploy-image.yaml‎

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jobs:
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build-and-push-image:
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runs-on:
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runs-on:
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- ubuntu-latest
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# - macos-latest
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permissions:
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steps:
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- name: Reset Docker & Buildx
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run: |
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docker buildx rm || true
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docker system prune -af
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docker builder prune -af
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docker buildx rm || true
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docker system prune -af
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docker builder prune -af
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- name: Free space
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run: |
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rm -rf /opt/hostedtoolcache
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echo "=============================================================================="
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echo "Freeing up disk space on CI system"
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echo "=============================================================================="
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rm -rf /opt/hostedtoolcache
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echo "=============================================================================="
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echo "Freeing up disk space on CI system"
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echo "=============================================================================="
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echo "Listing 100 largest packages"
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dpkg-query -Wf '${Installed-Size}\t${Package}\n' | sort -n | tail -n 100
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df -h
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echo "Removing large packages"
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sudo apt-get remove -y '^dotnet-.*'
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sudo apt-get remove -y '^llvm-.*'
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sudo apt-get remove -y 'php.*'
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sudo apt-get remove -y azure-cli google-cloud-sdk google-chrome-stable firefox powershell mono-devel
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sudo apt-get autoremove -y
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sudo apt-get clean
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df -h
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echo "Removing large directories"
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# deleting 15GB
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rm -rf /usr/share/dotnet/
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df -h
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echo "Listing 100 largest packages"
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dpkg-query -Wf '${Installed-Size}\t${Package}\n' | sort -n | tail -n 100
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df -h
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echo "Removing large packages"
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sudo apt-get remove -y '^dotnet-.*'
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sudo apt-get remove -y '^llvm-.*'
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sudo apt-get remove -y 'php.*'
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sudo apt-get remove -y azure-cli google-cloud-sdk google-chrome-stable firefox powershell mono-devel
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sudo apt-get autoremove -y
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sudo apt-get clean
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df -h
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echo "Removing large directories"
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# deleting 15GB
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rm -rf /usr/share/dotnet/
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df -h
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- name: Log in to the Container registry
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uses: docker/login-action@v3
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- name: Free disk space
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run: |
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docker system prune -af
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docker builder prune -af
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docker system prune -af
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docker builder prune -af
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- name: Debug build context
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run: du -sh .
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- name: Test
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run: docker run --rm ${{ steps.meta.outputs.tags }} python -c "import jax; print(jax.__version__)"
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- name: Push
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uses: docker/build-push-action@v6
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with:
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push: true
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}
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labels: ${{ steps.meta.outputs.labels }}

‎.gitignore‎

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# Saved checkpoints
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*/NDE_w_Standardization/
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*/checkpoints*/
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*/sbi-logs/
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*/sbi-logs/

‎.pre-commit-config.yaml‎

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exclude: ^(notebooks|logs)/
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repos:
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.13.0
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hooks:
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- id: ruff-check
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args: [--fix]
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- id: ruff-format
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- repo: https://github.com/pre-commit/mirrors-prettier
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rev: v3.1.0
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hooks:
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- id: prettier
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args: [--cache]
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v6.0.0
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hooks:
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- id: check-case-conflict
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description: Check for files that would conflict on a case-insensitive filesystem
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- id: check-docstring-first
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description: Check that the first line of a Python file is a docstring or a comment
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- id: check-merge-conflict
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description: Check for merge conflicts
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- id: check-toml
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description: Check TOML files for syntax errors
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- id: end-of-file-fixer
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description: Ensure files end with a newline character
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- id: mixed-line-ending
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args: [--fix=lf]
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description: Check for mixed line endings and fix them to LF
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- id: trailing-whitespace
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description: Check for trailing whitespace and fix it
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- id: check-added-large-files
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description: Check for large files added to the repository
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- id: check-symlinks
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description: Check for symbolic links which do not point to anything
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- id: detect-private-key
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description: Check for private keys in the repository

‎.readthedocs.yml‎

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- docs
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sphinx:
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configuration: docs/source/conf.py
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configuration: docs/source/conf.py

‎Dockerfile‎

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# Install system dependencies
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RUN apt-get update -y --quiet --fix-missing && \
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apt-get dist-upgrade -y --quiet --fix-missing && \
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apt-cache policy autconf && \
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apt-cache policy autconf && \
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apt-get install -y --quiet \
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apt-utils \
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autoconf \
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RUN pip install --no-cache-dir --upgrade pip && \
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pip install --no-cache-dir \
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jaxili==0.1.3
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jaxili==0.1.3

‎LICENSE‎

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The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

‎README.md‎

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[![Documentation](https://readthedocs.org/projects/jaxili/badge/?version=stable)](https://jaxili.readthedocs.io/en/stable)
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[![CI Test](https://github.com/sachaguer/jaxili/actions/workflows/ci.yml/badge.svg)]()
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[![black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
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[![PyPI](https://img.shields.io/pypi/v/jaxili)](https://pypi.org/project/jaxili/)
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[![black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
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[![PyPI](https://img.shields.io/pypi/v/jaxili)](https://pypi.org/project/jaxili/)
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![[PyPI - License](https://img.shields.io/pypi/l/jaxili)](https://github.com/sachaguer/jaxili/blob/main/LICENSE)
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This is a package to run Neural Density Estimation using Jax. The training is performed using `optax` (documentation available [here](https://optax.readthedocs.io/en/latest/)) and the neural network are created using `flax` (see [documentation](https://flax.readthedocs.io/en/latest/)).
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samples = posterior.sample(x=observation, num_samples=..., key=...) #You have to give a PRNGKey and specify the number of samples.
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```
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## Training a conditional MAF
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If you want to control the architecture of the network you can use the following code to train e.g. a Masked Autoregressive Flow (MAF).
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logger_params=logger_params,
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debug=debug,
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check_val_every_epoch=check_val_every_epoch,
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nde_class=nde_class
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nde_class=nde_class
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)
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#Train the Neural Density Estimator
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metrics_maf_npe = trainer_maf_npe.train_model(
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train_loader, val_loader, test_loader=test_loader, num_epochs=500, patience=20
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```
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The trained model can then be used to sample from or compute the log-probability of the learned distribution:
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```python

‎conda_env.yml‎

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- python=3.12
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- pip
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- pip:
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- jaxili
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- jaxili

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